Exploring genetic architecture of tick resistance in South African Nguni cattle

Mapholi, Ntanganedzeni Olivia (2015-12)

Thesis (PhD)--Stellenbosch University, 2015.

Thesis

ENGLISH ABSTRACT: The broad objective of this study was to identify single nucleotide polymorphisms (SNP) markers associated with tick resistance in South African Nguni cattle and it was addressed by three specific objectives. The first objective was to assess tick load and prevalence in Nguni cattle in different agro-climatic regions of South Africa using tick count data collected monthly from 586 Nguni cattle reared under natural grazing conditions, over two years. Tick counts were assessed under natural challenge at ARC Roodeplaat and Loskop farms (warm climate), and Mukhuthali Nguni Community and University of Fort Hare farms (cool climate). The second objective was to estimate genetic parameters for tick counts in Nguni cattle. The third objective was to identify SNPs associated with tick resistance in Nguni cattle. Counts for each tick species were conducted on each animal in the herd once a month on different body locations, including the head, ears, neck, back, legs, belly, perineum and tail. Distribution of counts was determined using the PROC FREQ (SAS, 2002 - 2010). The tick counts were then analysed with the PROC GLM procedure using the two fixed effect models. Genetic parameters for log-transformed counts were estimated from univariate animal and sire models and bivariate sire models using the ASREML program. Animals were genotyped using Illumina BovineSNP50K assay. After Quality Control (call rate >90%, minor allele frequency > 0.02), 40 436 SNPs were retained for analysis. Association analysis for tick resistance was carried out using two approaches: genome-wide association (GWA) analysis using the GenABEL package and a Regional Heritability Mapping (RHM) analysis. Six tick species were identified: Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) and Rhipicephalus simus (4%). Tick infestation was significantly affected by location, season, year, month of counting and age of the animal. Loskop farm, as the warmest location, had the highest tick counts and also showed the largest variation in tick loads. Higher tick counts were also observed in the hot-dry (September to November) and hot-wet (December to February) seasons compared to the other seasons. Amblyomma hebraeum was the dominant tick species across all four locations. Heritability estimates for tick count varied according to season and trait (body part or tick species) and ranged from 0.01±0.01 to 0.26±0.01. Genetic correlations ranged from -0.79±0.33 to 1.00±0.00 among counts for different body parts and 0.00±0.00 to 0.99±0.00 among tick species. Phenotypic correlations ranged from 0.06±0.01 to 0.72±0.01 among body parts and 0.01±0.02 to 0.44±0.01 for tick species. Whole body count was highly correlated to the perineum and the belly. These two traits appear to be the most suitable surrogates for whole body count. Several genomic regions of interest were identified for different traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total A. hebraeum ticks and for total number of A. hebraeum in the perineum region. Suggestive significant regions were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the tick traits analysed. The GWA approach identified more genomic regions than did the RHM approach. These findings provide information that would be useful in developing strategies for genetic improvement of tick resistance through selection. The chromosome regions identified as harbouring quantitative trait loci (QTL) underlying variation in tick burden form the basis for further analyses to identify specific candidate genes related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni.

AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om enkel nukleotied polimorfismes (ENPs) merkers te identifiseer wat verwant is aan bosluisweerstand in Suid-Afrikaanse Nguni beeste; dit is aangespreek deur drie doelwitte. Die eerste doelwit was om bosluislading en -voorkoms van bosluise in Nguni beeste in verskillende landbou-klimaatstreke van Suid-Afrika te bepaal deur die gebruik van bosluistelling data wat maandeliks van 586 Nguni beeste, grootgemaak op natuurlike weiding, oor 'n tydperk van twee jaar versamel was. Die tweede doelwit van die studie, was om die genetiese parameters te bepaal vir die bosluistellings in die Nguni beesras. Om hierdie doelwit aan te spreek, is vier verskillende datastelle onderskei in die bosluistelling data wat oor die twee jaar periode versamel was. Genetiese parameters is derhalwe beraam vir die telling van bosluise om sodoende die beste seisoen te identifiseer vir die insameling van bosluistelling data om ten einde strategieë te ontwikkel vir die genetiese seleksie vir vehoogde weerstand teen bosluise. Die derde doelwit was om ENP streke te identifiseer wat verband hou met bosluisweerstand in Nguni beeste. Verskillende bosluisspesies was getel op elke dier in die kudde een keer per maand op verskillende plekke op die liggaam, insluitend die kop, ore, nek, rug, bene, maag, perineum en stert. Bosluistelling data is ontleed met behulp van die SAS program om bosluislading variasie te bepaal. Genetiese parameter skattings vir log getransformeerde bosluistellings data was bereken vanaf twee-veranderlike vaar modelle en een-veranderlike dier- en vaar modelle met behulp van die ASREML program. Om ‘n genomiese wye assosiasie studie (GWAS) uit te voer, is DNS geïsoleer en genotipering gedoen met behulp van die Illumina BovineSNP50K toets. Na kwaliteit kontrole (oproep frekwensie>90%, klein alleelfrekwensie>0.02) is 40.436 ENPs behou vir ontleding. Assosiasie analise vir bosluisweerstand is uitgevoer met behulp twee benaderings, d.i. 'n genoom-wye assosiasie (GWA) analise met behulp van die GenABEL pakket en 'n plaaslike oorerflikheid karterings (POK) analise. Ses bosluisspesies is geïdentifiseer, d.i. Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) en Rhipicephalus simus (4%). Bosluis besmetting was beduidend beïnvloed deur die plek, seisoen, jaar, maand tel en ouderdom van die dier. Loskop plaas het die warmste weer ervaar en het die hoogste bosluis tellings en ook die grootste variasie in bosluislading gehad. Hoër bosluistellings is ook waargeneem in die warm droë (September tot November) en warm nat (Desember-Februarie) seisoene in vergelyking met die ander seisoene. Amblyomma hebraeum is geïdentifiseer as die mees dominante bosluisspesies oor al vier lokaliteite. Die voorkeur aanhegtingsarea vir die bosluise was onder die stert, perineum en maag areas op die liggaam. Die oorerflikheid beraming vir bosluistelling, soos beïnvloed deur die seisoen en eienskap (d.i. deel van die liggaam of bosluisspesies), het gewissel van 0.01±0.01 tot 0.26±0.01. Genetiese korrelasies het gewissel van -0.79±0.33 tot 1.04±0.01 vir bosluistellings op verskillende liggaamsdele en tussen 0.00±0.00 en 0.99±0.19 vir bosluisspesies. Fenotipiese korrelasies was laag tot matig en het gewissel van 0.06±0.01 tot 0.72±0.01 vir liggaamsdele en 0.01±0.02 to 0.44±0.01 vir bosluisspesies. Die datastel D wat September-Januarie bosluistellings bevat het die hoogste genetiese variasie aangedui. Heel liggaam bosluistellings was hoogs gekorreleerd met bosluistellings rondom die perineum en maag. Hierdie twee lokaliteite blyk die mees geskikte plaasvervanger vir die heel liggaam bosluistelling te wees. Verskeie genoom gebiede van belang is geïdentifiseer vir die verskillende eienskappe van beide die GWA en RHM benaderings. Drie genoom-wye beduidende streke (op chromosome 7, 10 en 19) is geïdentifiseer vir die totale bosluistelling op die kop, totale A. hebraeum bosluise en vir die totale aantal A. hebraeum in die perineum streek. Aanbevelende beduidende streke is geïdentifiseer op chromosome 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 en 26 vir 'n paar van die bosluis eienskappe wat ontleed was. Die GWA benadering identifiseer meer genoom gebiede as die POK benadering. Hierdie bevindinge bied nuttige inligting vir die ontwikkeling van strategieë vir die genetiese verbetering van bosluisweerstand deur seleksie. Die chromosome streke hier geïdentifiseer is skuiling kwantitatiewe eienskap loki (KEL) vir die onderliggende variasie in bosluislading en vorm die basis vir verdere ontledings vir spesifieke kandidaat gene te identifiseer wat verband hou met die vee bosluisweerstand en bied die potensiaal vir merkerbemiddelde seleksie in Nguni.

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